| 2006 Draft | ||||||
| Franchise Players | Franchise Players | |||||
| 1 | Ben | Bobby Abreu | 20 | Mike | Andruw Jones | |
| Bob | Jason Bay | 21 | Sonny | Todd Helton | ||
| Ben | Carlos Beltran | 22 | Mike | Paul Konerko | ||
| Jeremy | Lance Berkman | 23 | Sonny | Gary Sheffield | ||
| Jason | Miguel Cabrera | 24 | Bill | David Wright | ||
| JR | Johnny Damon | |||||
| Jason | Vladimir Guerrero | |||||
| David | Travis Hafner | |||||
| Denny | Derek Jeter | |||||
| Kris | Derek Lee | |||||
| Kris | David Ortiz | |||||
| Jeremy | Albert Pujols | |||||
| JR | Aramis Ramirez | |||||
| Bill | Alex Rodriguez | |||||
| David | Manny Ramirez | |||||
| Denny | Alphonso Soriano | |||||
| Jesse | Mark Teixiera | |||||
| Jesse | Miguel Tejada | |||||
| Bob | Michael Young | |||||
| Round 1 | Round 2 | |||||
| 25 | Mike | Carlos Lee | 37 | David | Jim Thome | |
| 26 | Ben | Hideki Matsui | 38 | Sonny | Hank Blalock | |
| 27 | JR | Adam Dunn | 39 | Jesse | Victor Martinez | |
| 28 | Bill | Ichiro Suzuki | 40 | Jason | Aubrey Huff | |
| 29 | Jeremy | Carl Crawford | 41 | Kris | Ryan Zimmerman | |
| 30 | Bob | Richie Sexson | 42 | Denny | Eric Chavez | |
| 31 | Denny | Ken Griffey Jr | 43 | Bob | Morgan Ensberg | |
| 32 | Kris | Matt Holliday | 44 | Jeremy | Grady Sizemore | |
| 33 | Jason | Carlos Delgado | 45 | Bill | Jeff Kent | |
| 34 | Jesse | Chase Utley | 46 | JR | Jorge Posada | |
| 35 | Sonny | Chone Figgins | 47 | Ben | Jorge Cantu | |
| 36 | David | Vernon Wells | 48 | Mike | Scott Podsednik | |
| Round 3 | Round 4 | |||||
| 49 | Mike | Juan Pierre | 61 | David | Jason Varitek | |
| 50 | Ben | Edgar Renteria | 62 | Sonny | Joe Mauer | |
| 51 | JR | Nomar Garciaparra | 63 | Jesse | Barry Bonds | |
| 52 | Bill | Pat Burrell | 64 | Jason | Mark Loretta | |
| 53 | Jeremy | Jose Reyes | 65 | Kris | Carlos Guillen | |
| 54 | Bob | Marcus Giles | 66 | Denny | Torii Hunter | |
| 55 | Denny | Richie Weeks | 67 | Bob | Brad Wilkerson | |
| 56 | Kris | Magglio Ordonez | 68 | Jeremy | Melvin Mora | |
| 57 | Jason | Scott Rolen | 69 | Bill | Felipe Lopez | |
| 58 | Jesse | Coco Crisp | 70 | JR | Brian Roberts | |
| 59 | Sonny | Jimmie Rollins | 71 | Ben | Troy Glaus | |
| 60 | David | Johnny Peralta | 72 | Mike | Rafael Furcal | |
| Round 5 | Round 6 | |||||
| 73 | Mike | Ryan Howard | 85 | David | Robinson Cano | |
| 74 | Ben | Jason Giambi | 86 | Sonny | Preston Wilson | |
| 75 | JR | Chipper Jones | 87 | Jesse | Garrett Anderson | |
| 76 | Bill | Cliff Floyd | 88 | Jason | Chad Tracy | |
| 77 | Jeremy | Tadahito Iguchi | 89 | Kris | Placido Polanco | |
| 78 | Bob | Brian Giles | 90 | Denny | Willie Tavarez | |
| 79 | Denny | Ivan Rodriguez | 91 | Bob | Pedro Feliz | |
| 80 | Kris | Randy Winn | 92 | Jeremy | Jeff Francoeur | |
| 81 | Jason | Clint Barmes | 93 | Bill | Geoff Jenkins | |
| 82 | Jesse | Adrian Beltre | 94 | JR | Shawn Green | |
| 83 | Sonny | Jim Edmonds | 95 | Ben | Aaron Rowand | |
| 84 | David | Jermaine Dye | 96 | Mike | Shea Hillenbrand | |
| Round 7 | Round 8 | |||||
| 97 | Mike | Ryan Freel | 109 | David | Edwin Encarncion | |
| 98 | Ben | Jason Kendall | 110 | Sonny | Lyle Overbay | |
| 99 | JR | Dmitri Young | 111 | Jesse | Luis Gonzalez | |
| 100 | Bill | Ben Molina | 112 | Jason | Mike Piazza | |
| 101 | Jeremy | Jonny Gomes | 113 | Kris | Paul LoDuca | |
| 102 | Bob | Kevin Mench | 114 | Denny | Milton Bradley | |
| 103 | Denny | Nick Johnson | 115 | Bob | Bobby Crosby | |
| 104 | Kris | Moises Alou | 116 | Jeremy | Javy Lopez | |
| 105 | Jason | Jose Guillen | 117 | Bill | Jeromy Burnitz | |
| 106 | Jesse | JD Drew | 118 | JR | Shannon Stewart | |
| 107 | Sonny | Austin Kearns | 119 | Ben | Ben Broussard | |
| 108 | David | Raul Ibanez | 120 | Mike | Mike Barrett | |
| Round 9 | Round 10 | |||||
| 121 | Mike | Wily Mo Pena | 133 | David | Craig Monroe | |
| 122 | Ben | Jay Gibbons | 134 | Sonny | Prince Fielder | |
| 123 | JR | Craig Biggio | 135 | Jesse | Rocco Baldelli | |
| 124 | Bill | Mike Sweeney | 136 | Jason | Kenji Johjima | |
| 125 | Jeremy | Dan Johnson | 137 | Kris | Garrett Atkins | |
| 126 | Bob | Jeremy Hermida | 138 | Denny | Sean Casey | |
| 127 | Denny | Mark Ellis | 139 | Bob | Ramon Hernandez | |
| 128 | Kris | Mark Grudzielanek | 140 | Jeremy | Mike Lowell | |
| 129 | Jason | Jason Lane | 141 | Bill | Adam LaRoche | |
| 130 | Jesse | Jacques Jones | 142 | JR | Chris Burke | |
| 131 | Sonny | Reggie Sanders | 143 | Ben | Adam Eckstein | |
| 132 | David | Justin Morneau | 144 | Mike | Chris Shelton | |
| Round 11 | Round 12 | |||||
| 145 | Mike | Ronny Cedeno | 157 | David | Aaron Boone | |
| 146 | Ben | Mark Kotsay | 158 | Sonny | Jose Vidro | |
| 147 | JR | A.J. Pierzynski | 159 | Jesse | Luis Castillo | |
| 148 | Bill | Emil Brown | 160 | Jason | Jose Castillo | |
| 149 | Jeremy | Ian Kinsler | 161 | Kris | Brady Clark | |
| 150 | Bob | Ronnie Belliard | 162 | Denny | Frank Thomas | |
| 151 | Denny | Khalil Greene | 163 | Bob | Nick Swisher | |
| 152 | Kris | David DeJesus | 164 | Jeremy | Orlando Cabrera | |
| 153 | Jason | Juan Uribe | 165 | Bill | Luis A. Gonzalez | |
| 154 | Jesse | Phil Nevin | 166 | JR | Joe Crede | |
| 155 | Sonny | Angel Berroa | 167 | Ben | Corie Koskie | |
| 156 | David | Julio Lugo | 168 | Mike | Ray Durham | |
| Round 13 | Round 14 | |||||
| 169 | Mike | Matt Murton | 181 | David | Casey Blake | |
| 170 | Ben | D'Angelo Jimenez | 182 | Sonny | Mike Cameron | |
| 171 | JR | Jose Valentin | 183 | Jesse | Russ Adams | |
| 172 | Bill | Adam Everett | 184 | Jason | Curtis Granderson | |
| 173 | Jeremy | Brian McCann | 185 | Kris | Mike Lieberthal | |
| 174 | Bob | Greg Zaun | 186 | Denny | Bill Mueller | |
| 175 | Denny | Trot Nixon | 187 | Bob | Kevin Youkilis | |
| 176 | Kris | Rondell White | 188 | Jeremy | Alex Rios | |
| 177 | Jason | Casey Kotchman | 189 | Bill | Brian Schneider | |
| 178 | Jesse | Josh Willingham | 190 | JR | Javier Valentin | |
| 179 | Sonny | David Dellucci | 191 | Ben | J.J. Hardy | |
| 180 | David | Rod Barajas | 192 | Mike | Bill Hall | |
| Round 15 | Round 16 | |||||
| 193 | Mike | Cory Patterson | 205 | David | Juan Encarncion | |
| 194 | Ben | Carl Everett | 206 | Sonny | Yorvit Torrelba | |
| 195 | JR | Bobby Higginson | 207 | Jesse | Jason Micheals | |
| 196 | Bill | Dallas McPherson | 208 | Jason | Lance Niekro | |
| 197 | Jeremy | Mike Jacobs | 209 | Kris | Ryan Klesko | |
| 198 | Bob | Jason Kubel | 210 | Denny | Hanley Ramirez | |
| 199 | Denny | Brandon Inge | 211 | Bob | Cory Sullivan | |
| 200 | Kris | Craig Counsell | 212 | Jeremy | Johnny Estrada | |
| 201 | Jason | Delwyn Young | 213 | Bill | Jose Cruz Jr. | |
| 202 | Jesse | Tony Batista | 214 | JR | Mike Lamb | |
| 203 | Sonny | Brian Anderson | 215 | Ben | Xavier Nady | |
| 204 | David | Orlando Hudson | 216 | Mike | Todd Walker | |
